Yuto Uesugi | Collective Animal Behavior

Recently, I participated in a journal club on active matter, held as part of the "Seminar in Physics" course for third-year undergraduate students in the Department of Physics at the University of Tokyo. The seminar is supervised by Professor Takeuchi, who is also my supervisor. Along with Uesugi and two B3 students, we read a recent review paper on active matter [1].

In Chapters 1 and 2, we learned the basic concepts of active matter, focusing on theoretical aspects such as Polar Flocks and Active Nematics. From Chapter 3 to Chapter 8, various specific systems were introduced with experimental examples (we covered Chapters 3 to 6). Uesugi was responsible for Chapter 4, "Motion of Microorganisms."

Overall, the review paper presented a plethora of specific examples, making it somewhat challenging to grasp an overarching perspective. However, the abundance of concrete cases made it a valuable starting point for delving deeper into topics of interest. Below are some notable points that left an impression on me:

Run-and-tumble is realized through flagellar filament shape changes: The run-and-tumble motion observed in prokaryotes is achieved by switching the rotation direction of flagella, which is based on a physical mechanism where the shape of the flagellar filament changes according to the rotation direction. The flagellar filament consists of 11 protofilaments arranged in a cylindrical structure, with two types: L-type and R-type (left-handed and right-handed), which have slightly different lengths. When the flagellar motor switches rotation direction, the ratio of L-type to R-type protofilaments changes, resulting in a different filament shape [4.1 Prokaryotic Flagella].

Chlamydomonas flagellar synchronization: The two flagella of Chlamydomonas synchronize through fluid interactions [2], which has been confirmed through experiments involving mutants with only one flagellum placed in close proximity [3] [4.3 Synchronization].

Quorum sensing: Bacteria communicate chemically by producing and detecting signaling molecules. Specifically, they estimate the density of surrounding individuals based on the concentration of these chemicals and change their behavior collectively once a certain threshold is exceeded. This mechanism enables bacteria to coordinate collective behaviors such as aggregation [4.4 Bacterial Suspensions].

Division of labor and cooperation within monospecies biofilms: Even in biofilms composed of a single bacterial species, there is a division of roles between peripheral bacteria, which have easier access to external nutrients but are more vulnerable to external threats, and internal bacteria, which are in a starved state but more resistant to threats. When peripheral bacteria die, internal bacteria grow to replenish the periphery. Additionally, in environments without external threats, peripheral bacteria periodically halt their growth to allocate nutrients to internal bacteria, preventing mass starvation of the latter [4] [4.7 Biofilms].

References

[1] L. Pismen, "Active Matter Within and Around Us: From Self-Propelled Particles to Flocks and Living Forms" Springer Cham (2021). https://link.springer.com/book/10.1007/978-3-030-68421-1

[2] B. Friedrich, "Hydrodynamic synchronization of flagellar oscillators", Eur. Phys. J. Spec. Top. 225, 2353 (2016).

[3] D. R. Brumley, K. Y. Wan, M. Polin, and R. E. Goldstein, "Flagellar synchronization through direct hydrodynamic interactions", eLife 3, e02750 (2014).

[4] J. Liu, A. Prindle, J. Humphries, M. Gabalda-Sagarra, M. Asally, D. D. Lee, S. Ly, J. Garcia-Ojalvo, and G. M. Süel, "Metabolic co-dependence gives rise to collective oscillations within biofilms", Nature 523, 550 (2015).